RGA ELAND basic version can be downloaded here. Usage.

RGA - Reference Guided Assember. It does:
  1. calcuate the real coverage of Solexa microreads to the reference sequence(s)

  2. report the coordinates of all the maximum contigs and length

  3. output density graphes of chromosome size

RGA BLAT basic version can be downloaded here. Usage.

RGA - Reference Guided Assember. It does:
  1. calcuate the real coverage of Solexa microreads to the reference sequence(s)

  2. report the coordinates of all the maximum contigs and length

  3. output density graphes of chromosome size

RGA BLAT version with SNP detection (Q values are required) can be downloaded here. Usage.

RGA - Reference Guided Assember. It does:
  1. calcuate the real coverage of Solexa microreads to the reference sequence(s)

  2. report the coordinates of all the maximum contigs and length

  3. output density graphes of chromosome size

  4. incorporate the Q values

  5. output contigs

  6. output SNPs

BLAT executable can be downloaded here. BLAT is from Jim Kent @ UCSC.

More information about using BLAT and .ooc file.

Gnuplot executable v4.2.2 can be downloaded here.

Please contact Rongkun Shen with any questions, concerns, or comments you may have regarding RGA.